Defective activation and regulation of type I interferon immunity is associated with increasing COVID-19 severity

Host immunity to infection with SARS-CoV-2 is highly variable, dictating diverse clinical outcomes ranging from asymptomatic to severe disease and death. We previously reported reduced type I interferon in severe COVID-19 patients preceded clinical worsening. Further studies identified genetic mutations in loci of the TLR3- or TLR7-dependent interferon-I pathways, or neutralizing interferon-I autoantibodies as risk factors for development of COVID-19 pneumonia. Here we show in patient cohorts with different severities of COVID-19, that baseline plasma interferon α measures differ according to the immunoassay used, timing of sampling, the interferon α subtype measured, and the presence of autoantibodies. We also show a consistently reduced induction of interferon-I proteins in hospitalized COVID-19 patients upon immune stimulation, that is not associated with detectable neutralizing autoantibodies against interferon α or interferon ω. Intracellular proteomic analysis shows increased monocyte numbers in hospitalized COVID-19 patients but impaired interferon-I response after stimulation. We confirm this by ex vivo whole blood stimulation with interferon-I which induces transcriptomic responses associated with inflammation in hospitalized COVID-19 patients, that is not seen in controls or non-hospitalized moderate cases. These results may explain the dichotomy of the poor clinical response to interferon-I based treatments in late stage COVID-19, despite the importance of interferon-I in early acute infection and may guide alternative therapeutic strategies.


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Sex was included in biological analysis as much as possible, as sex is a known factor associated with COVID-19 severity. Sex information on patients is included in the data files.
Age, sex, and clinical status is provided for all donors and patients. No genetic information was collected.
Patients were recruited at different clinical centres as described in the methods, based on classical clinical characteristics for defining SARS-CoV-2 infectivity (PCR based test).
For the Irish studies ethical approval was obtained for the study from the Tallaght University Hospital (TUH)/St James's Hospital (SJH) Joint Research Ethics Committee (reference REC 2020-03). For the French studies samples were obtained from Hopital Cochin and Hopital Bichat, Paris under clinical study protocols in the setting of the local RADIPEM biological samples collection, derived from samples collected in routine care as previously described , or from the INSERM-sponsored French COVID-19 clinical study (NCT04262921). Biological collection and informed consent were approved by the Direction de la Recherche Clinique et Innovation and the French Ministry of Research (no. 2019Research (no. -3677, 2020. The studies conformed to the principles outlined in the Declaration of Helsinki, and received approval by the appropriate Institutional Review Boards (Cochin-Port Royal Hospital, Paris; no AAA-2020-08018 and Comité de protection des personnes Ile de France VI; no 2020-A00256-33).
Sample sizes were chosen based on previously published studies on IFN immunity in COVID-19 patients and the expected effect size differences in IFN-I associated phenotypes (Hadjadj et al Science 2020) Generated data was not excluded, in certain analyses were sample volume was too low certain patients were not included in those specific analyses.
Specific assays were qualified at the point of assay development (prior to this study) to ensure repeatability and reproducibility. For initial findings in one cohort, they were replicated in additional independent cohorts. Allocation was not randomized as patients were included in specific groups based on clinical pehnotypes (notbaly requirement for supplmental oxygen). However attempts were made to balance patient groups as much as possible in terms of age and sex.
Blinding was not possible as samples were labelled by clinicians, and then handled by experimentalists who analyzed the data sets. CD3 APC-H7 ref. 560176 BD: The SK7 (Leu-4) monoclonal antibody specifically binds to the epsilon chain of the CD3 antigen/T-cell antigen receptor (TCR) complex. This complex is composed of at least six proteins that range in molecular weight from 20 to 30 kDa. The antigen recognized by CD3 antibodies is noncovalently associated with either !/" or #/$ TCR (70 to 90 kDa). CD19 BV711 ref. 563036 BD: The SJ25C1 monoclonal antibody specifically binds to CD19, a B lymphocyte-lineage differentiation antigen. CD19, a 90-kDa transmembrance glycoprotein, is a member of the immunoglobulin superfamily and is expressed throughout B-lymphocyte development from the pro-B cell through the mature B-cell stages.
CCD56 BV586 ref. 557747 BD: The B159 monoclonal antibody specifically binds to CD56. CD56 is a heavily glycosylated adhesion protein that is present on a subpopulation of peripheral blood large granular lymphocytes that demonstrate natural killer activity. CD56 is also expressed on a subset of T cells but is not expressed on myeloid cells, erythrocytes or B cells. This antigen is a pan-NKcell marker. CD56 is virtually identical to an isoform of the neural cell adhesion molecule (NCAM), a structure mediating homotypic and heterotypic cell-cell interactions.
CD14 PE.cy7 ref. 561391 BD: The CD14 antibody, clone M'P9, is derived from the hybridization of Sp2/0 mouse myeloma cells with spleen cells from BALB/c mice immunized with peripheral blood monocytes from a patient with rheumatoid arthritis. The CD14 antibody binds specifically to the 53-55 kilodalton (kDa) glycosylphosphatidylinositol (GPI)-anchored single-chain glycoprotein, CD14, also known as the LPS receptor or LPS-R.
CD16 PE-CF594 ref. 562293 BD: The 3G8 monoclonal antibody specifically recognizes CD16a and CD16b, low affinity receptors for the Fc region of IgG. CD16a is~50-65 kDa type I transmembrane glycoprotein that is encoded by FCGR3A (Fc fragment of IgG receptor IIIa) which belongs to the immunoglobulin superfamily. CD16a is also known as Fc-gamma RIII-alpha (Fc-gamma RIIIa or Fc#RIIIA) or FcRIIIa and is expressed on natural killer cells, activated monocytes, macrophages, #$ T cells, immature thymocytes, and mast cells. CD16a binds immune-complexed or aggregated IgG and associates with CD247/TCR& in NK cells and Fc%RI# chains in phagocytes and mast cells to transduce intracellular signals. CD16a functions in antibody-dependent cellular cytotoxicity (ADCC) and other antibody-dependent responses including phagocytosis, cytokine production or mediator release. CD16b is a~48 kDa glycophosyl-phosphatidylinositol (GPI)-linked form that is encoded by FCGR3B (Fc fragment of IgG receptor IIIb). CD16b is also known as Fc-gamma RIII-beta (Fc-gamma RIIIb or Fc#RIIIB) or FcRIIIb and is expressed on neutrophils and activated eosinophils. The extracellular region of CD16b is highly homologous to CD16a. CD16b also serves as a receptor for the Fc region of IgG and can bind immune-complexed or aggregated IgG and may be involved in neutrophil adhesion.
CCD66b Pacific Blue ref. 562940 BD: The G10F5 monoclonal antibody specifically binds to CD66b, also known as Carcinoembryonic antigen-related cell adhesion molecule 8 (CEACAM8). CD66b is a glycosylphosphatidylinositol (GPI) linked protein with a molecular weight of 100 kDa expressed on granulocytes. This molecule was previously clustered as CD67 in the Fourth Human Leucocyte Differentiation Antigen (HLDA) Workshop and renamed CD66b in the Fifth HLDA Workshop. CD66b is a member of the carcinoembryonic antigen (CEA)-like glycoprotein family present on granulocytes and referred to as non-specific crossreacting antigens (NCA). Granulocyte activation induced with soluble stimulators (calcium ionophore, phorbol myristate acetate, Nformylmethionyl-leucyl-phenylalanine) results in release and increased expression of NCA. Findings suggest that these molecules may play a role in phagocytosis, chemotaxis and adherence.